Hmm file for illumina cytoSNP 850K array

WGLab / PennCNV

Copy number vaiation detection from SNP arrays

http://penncnv.openbioinformatics.org

Other

89 stars 55 forks source link

Hmm file for illumina cytoSNP 850K array #84

Open Sneha-bioinfo opened 2 years ago

Sneha-bioinfo commented 2 years ago

I'm working on cancer samples run on illumina cytoSNP 850K array ( probes designed on GRCh38). I am trying to use PennCNV to detect the copy number variation from the data. Which hmm file would be appropriate for this? I couldn't find any hmm file trained on GRCh38 in the site.

kaichop commented 2 years ago

For Illumina arrays, you can just use hall.hmm. It is not related to genome coordinate. Also make sure you make PFB file using compile_pfb.pl and using the signal files with GRCh38 coordinate.

On Sat, May 14, 2022 at 1:11 PM Sneha Das @.***> wrote:

I'm working on cancer samples run on illumina cytoSNP 850 array ( probes designed on GRCh38). I am trying to use PennCNV to detect the copy number variation from the data. Which hmm file would be appropriate for this? I couldn't find any hmm file trained on GRCh38 in the site.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/84, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCQ5B2L2VAY2EEXS6DVJ7NE3ANCNFSM5V52SYHQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

chopraamhk commented 2 years ago

Dear Developer,

Which .hmm file should I use against Affymetrix Precision Medicine Research Array?

kaichop commented 2 years ago

This is Axiom array. You may want to read the paper below and follow the procedures there.

20161024: Prof. George Kirov shared a recently published paper reporting the use of PennCNV on Affy Axiom arrays here https://pubmed.ncbi.nlm.nih.gov/27773354/. Detailed procedure for CNV calling is given in the supplementary materials.

On Mon, May 23, 2022 at 9:57 PM Mehak Chopra @.***> wrote:

Dear Developer,

Which .hmm file should I use against Affymetrix Precision Medicine Research Array?

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/84#issuecomment-1135315978, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGU7NT4SFZS5KGTOGTVLQZRFANCNFSM5V52SYHQ . You are receiving this because you commented.Message ID: @.***>